I have done as you asked and checked your script:
/usr/local/ispconfig/server/cron_daily.php

It seems it's your SQL query that's faulty. If you think it works properly, then you have missed this logical error.

You use this query to check for the month's traffic, which will return a row-set of dates:

PHP:

SELECT traffic_bytes FROM web_traffic WHERE traffic_date like '$current_month%' AND hostname = '$domain'

So when you run the below PHP code, you only retrieve the traffic from the first date of current month:

PHP:

$web_traffic = $tmp['traffic_bytes']/1024/1024;

Which should be cast to int by the way:

PHP:

$web_traffic = (int)$tmp['traffic_bytes']/1024/1024;

It looks to me like you really meant to use an SQL statement like this instead to return all the month's bytes in 1 row. This will return all the month's traffic, and with the rest of your PHP code compare it correctly against the traffic_quota column from the table web_domain:

PHP:

SELECT SUM(traffic_bytes) As total_traffic_bytes FROM web_traffic WHERE traffic_date like '$current_month%' AND hostname = '$domain'

And change the $web_traffic code to:

PHP:

$web_traffic = (int)$tmp['total_traffic_bytes']/1024/1024;

To put it simple, your script currently only locks a site if the first day of traffic for the current month is over the traffic quota that is supposed to be for the whole month. I have made these modifications to your script in my version of ISP Config, and it works properly now if I run: /usr/local/ispconfig/server/cron_daily.sh